I'm seeing something very similar with 1.16.1

aborting commit write group: KeyError('specification-20090527025523-61x6cd872383vbos-2',)
bzr: ERROR: exceptions.KeyError: 'specification-20090527025523-61x6cd872383vbos-2'                                                                          

Traceback (most recent call last):
  File "/usr/lib/python2.6/dist-packages/bzrlib/commands.py", line 729, in exception_to_return_code
    return the_callable(*args, **kwargs)
  File "/usr/lib/python2.6/dist-packages/bzrlib/commands.py", line 924, in run_bzr
    ret = run(*run_argv)
  File "/usr/lib/python2.6/dist-packages/bzrlib/commands.py", line 560, in run_argv_aliases
    return self.run(**all_cmd_args)
  File "/usr/lib/python2.6/dist-packages/bzrlib/builtins.py", line 2937, in run
    exclude=safe_relpath_files(tree, exclude))
  File "/usr/lib/python2.6/dist-packages/bzrlib/decorators.py", line 192, in write_locked
    result = unbound(self, *args, **kwargs)
  File "/usr/lib/python2.6/dist-packages/bzrlib/workingtree_4.py", line 226, in commit
    result = WorkingTree3.commit(self, message, revprops, *args, **kwargs)
  File "/usr/lib/python2.6/dist-packages/bzrlib/decorators.py", line 192, in write_locked
    result = unbound(self, *args, **kwargs)
  File "/usr/lib/python2.6/dist-packages/bzrlib/mutabletree.py", line 228, in commit
    *args, **kwargs)
  File "/usr/lib/python2.6/dist-packages/bzrlib/commit.py", line 363, in commit
    self._update_builder_with_changes()
  File "/usr/lib/python2.6/dist-packages/bzrlib/commit.py", line 644, in _update_builder_with_changes
    self.work_tree, self.basis_revid, iter_changes):
  File "/usr/lib/python2.6/dist-packages/bzrlib/repository.py", line 638, in record_iter_changes
    for change in iter_changes:
  File "/usr/lib/python2.6/dist-packages/bzrlib/commit.py", line 700, in _filter_iter_changes
    self.work_tree.unversion(deleted_ids)
  File "/usr/lib/python2.6/dist-packages/bzrlib/mutabletree.py", line 52, in tree_write_locked
    return unbound(self, *args, **kwargs)
  File "/usr/lib/python2.6/dist-packages/bzrlib/workingtree_4.py", line 1260, in unversion
    self._inventory.remove_recursive_id(file_id)
  File "/usr/lib/python2.6/dist-packages/bzrlib/inventory.py", line 1396, in remove_recursive_id
    to_find_delete = [self._byid[file_id]]
KeyError: 'specification-20090527025523-61x6cd872383vbos-2'

bzr 1.16.1 on python 2.6.2 (linux2)
arguments: ['/usr/bin/bzr', 'commit', '-m', 'upgrade gems and create new cucumber environment']
encoding: 'UTF-8', fsenc: 'UTF-8', lang: 'en_AU.UTF-8'
plugins:
  builddeb             /usr/lib/python2.6/dist-packages/bzrlib/plugins/builddeb [unknown]
  bzrtools             /usr/lib/python2.6/dist-packages/bzrlib/plugins/bzrtools [1.16]
  launchpad            /usr/lib/python2.6/dist-packages/bzrlib/plugins/launchpad [1.16.1]
  netrc_credential_store /usr/lib/python2.6/dist-packages/bzrlib/plugins/netrc_credential_store [1.16.1]
  svn                  /usr/lib/python2.6/dist-packages/bzrlib/plugins/svn [0.6.2]
*** Bazaar has encountered an internal error.
    Please report a bug at https://bugs.launchpad.net/bzr/+filebug
    including this traceback, and a description of what you
    were doing when the error occurred.